[AMBER] process_mdout.perl script

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Tue, 3 May 2016 15:35:47 +0200

Dear Amber users,

When analysing my output files with the script “process_mdout.perl”, I find that it is not retrieving the density, nor the volume, of my system as both summary.DENSITY and summary.VOLUME files only contain the time elapsed. Am I using an “old” version? I send it to you in attachements.

This is the input that produces the output file I’m trying to analyse:

Constant Temp 300K Pres 1.0 MD
 &cntrl
  imin=0,
  irest=1, ntx=5,
  ntb=2, pres0=1.0, ntp=1, taup=1.0,
  cut=12.0,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=2.0,
  nstlim=50000, dt=0.001,
  ntpr=500, ntwx=200, ntwr=10000,
  ntc=2, ntf=2,
  noshakemask = '.474-494,521-534,900-909,917-933,2646-2689,2828-2851,2931-2936’,
  ntr=1,
  restraintmask = ':170,185,.CA,C,N',
  restraint_wt=5.0,
  ifqnt=1,
 /
 &qmmm
  qmmask=':32,35,59,61,168,169,179,186-187,1007,2332,2637',
  qmcharge=-1,
  qm_theory='PM3',
  qmshake=0,
  qmcut=12.0,
 /

Thanks for any help!

Ruth



     

         



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Received on Tue May 03 2016 - 07:00:03 PDT
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